[2024-01-24 13:09:51,514] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:51,518] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:51,518] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b22d765-9bf7-48ef-9c97-2662dc3895ba/dqc_reference
[2024-01-24 13:09:52,883] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:52,884] [INFO] Task started: Prodigal
[2024-01-24 13:09:52,884] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1b94f65-93be-4531-b6df-fbbb77c6f3fb/GCF_009936235.1_ASM993623v1_genomic.fna.gz | prodigal -d GCF_009936235.1_ASM993623v1_genomic.fna/cds.fna -a GCF_009936235.1_ASM993623v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:09,316] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:09,316] [INFO] Task started: HMMsearch
[2024-01-24 13:10:09,317] [INFO] Running command: hmmsearch --tblout GCF_009936235.1_ASM993623v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b22d765-9bf7-48ef-9c97-2662dc3895ba/dqc_reference/reference_markers.hmm GCF_009936235.1_ASM993623v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:09,599] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:09,600] [INFO] Found 6/6 markers.
[2024-01-24 13:10:09,641] [INFO] Query marker FASTA was written to GCF_009936235.1_ASM993623v1_genomic.fna/markers.fasta
[2024-01-24 13:10:09,641] [INFO] Task started: Blastn
[2024-01-24 13:10:09,642] [INFO] Running command: blastn -query GCF_009936235.1_ASM993623v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b22d765-9bf7-48ef-9c97-2662dc3895ba/dqc_reference/reference_markers.fasta -out GCF_009936235.1_ASM993623v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:10,704] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:10,708] [INFO] Selected 7 target genomes.
[2024-01-24 13:10:10,708] [INFO] Target genome list was writen to GCF_009936235.1_ASM993623v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:10,712] [INFO] Task started: fastANI
[2024-01-24 13:10:10,712] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1b94f65-93be-4531-b6df-fbbb77c6f3fb/GCF_009936235.1_ASM993623v1_genomic.fna.gz --refList GCF_009936235.1_ASM993623v1_genomic.fna/target_genomes.txt --output GCF_009936235.1_ASM993623v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:20,170] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:20,171] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b22d765-9bf7-48ef-9c97-2662dc3895ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:20,171] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b22d765-9bf7-48ef-9c97-2662dc3895ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:20,179] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:10:20,179] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:20,179] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Mycobacterium xenopi	strain=JCM 15661T	GCA_009936235.1	1789	1789	type	True	100.0	1639	1639	95	conclusive
Mycobacterium xenopi	strain=NCTC10042	GCA_900453395.1	1789	1789	type	True	99.9827	1626	1639	95	conclusive
Mycobacterium xenopi	strain=DSM 43995	GCA_002102015.1	1789	1789	type	True	99.905	1513	1639	95	conclusive
Mycobacterium heckeshornense	strain=JCM 15655	GCA_016592155.1	110505	110505	type	True	90.2897	1324	1639	95	below_threshold
Mycobacterium noviomagense	strain=DSM 45145	GCA_002086415.1	459858	459858	type	True	84.2538	1118	1639	95	below_threshold
Mycobacterium lacus	strain=DSM 44577	GCA_002102215.1	169765	169765	type	True	79.9408	783	1639	95	below_threshold
Mycobacterium lacus	strain=JCM 15657	GCA_010731535.1	169765	169765	type	True	79.8709	815	1639	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:20,181] [INFO] DFAST Taxonomy check result was written to GCF_009936235.1_ASM993623v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:20,181] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:20,181] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:20,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b22d765-9bf7-48ef-9c97-2662dc3895ba/dqc_reference/checkm_data
[2024-01-24 13:10:20,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:20,231] [INFO] Task started: CheckM
[2024-01-24 13:10:20,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009936235.1_ASM993623v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009936235.1_ASM993623v1_genomic.fna/checkm_input GCF_009936235.1_ASM993623v1_genomic.fna/checkm_result
[2024-01-24 13:11:07,713] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:07,714] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:07,736] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:07,737] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:07,737] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009936235.1_ASM993623v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:07,737] [INFO] Task started: Blastn
[2024-01-24 13:11:07,738] [INFO] Running command: blastn -query GCF_009936235.1_ASM993623v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b22d765-9bf7-48ef-9c97-2662dc3895ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_009936235.1_ASM993623v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:09,151] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:09,156] [INFO] Selected 16 target genomes.
[2024-01-24 13:11:09,156] [INFO] Target genome list was writen to GCF_009936235.1_ASM993623v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:09,168] [INFO] Task started: fastANI
[2024-01-24 13:11:09,168] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1b94f65-93be-4531-b6df-fbbb77c6f3fb/GCF_009936235.1_ASM993623v1_genomic.fna.gz --refList GCF_009936235.1_ASM993623v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009936235.1_ASM993623v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:28,358] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:28,384] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:28,384] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_009936235.1	s__Mycobacterium xenopi	100.0	1639	1639	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.67	99.09	0.97	0.94	5	conclusive
GCF_016592155.1	s__Mycobacterium heckeshornense	90.2805	1325	1639	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.54	99.17	0.94	0.93	4	-
GCF_010731635.1	s__Mycobacterium noviomagense	84.2963	1162	1639	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002101735.1	s__Mycobacterium kyorinense	81.6835	997	1639	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.84	99.84	0.96	0.94	3	-
GCF_002101595.1	s__Mycobacterium celatum	81.5885	998	1639	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003402475.1	s__Mycobacterium sp003402475	81.4941	998	1639	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102185.1	s__Mycobacterium fragae	80.8155	963	1639	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101785.1	s__Mycobacterium palustre	80.5489	870	1639	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086635.1	s__Mycobacterium alsense	80.405	870	1639	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.76	96.71	0.91	0.90	3	-
GCF_001668725.1	s__Mycobacterium sp001668725	80.2811	859	1639	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.46	99.46	0.97	0.97	2	-
GCA_002101905.1	s__Mycobacterium shimoidei	80.192	863	1639	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.72	99.46	0.97	0.95	3	-
GCF_001954275.1	s__Mycobacterium sp001954275	80.0872	839	1639	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.75	98.75	0.90	0.90	2	-
GCF_001665295.1	s__Mycobacterium sp001665295	80.0793	875	1639	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001053185.1	s__Mycobacterium bohemicum	79.9589	799	1639	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_010731535.1	s__Mycobacterium lacus	79.8922	811	1639	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCA_019236925.1	s__Mycobacterium sp019236925	79.6317	728	1639	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:28,386] [INFO] GTDB search result was written to GCF_009936235.1_ASM993623v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:28,386] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:28,389] [INFO] DFAST_QC result json was written to GCF_009936235.1_ASM993623v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:28,389] [INFO] DFAST_QC completed!
[2024-01-24 13:11:28,389] [INFO] Total running time: 0h1m37s